Added allele difference calculation to Axiom Copy Number analysis.
Enabled wave correction for copy number analysis.
Added parameters to input a covariate adjustment file.
Added parameter to enable SNPQC calculation.
Enabled wave correction when creating a reference model file for AxiomCN.
The 2.11.2 APT release is a point release to update apt-copynumber-axiom-ref, apt-copynumber-axiom-safer, apt-copynumber-axiom-cnvmix, apt-copynumber-axiom-hmm, apt-copynumber-cyto-ssa and apt-copynumber-familial to support ChAS 4.1. Version: apt-2.11.2 Date: Thursday February 27, 2020
Add rare-het-calling dev parameter to the header of the output files as usual.
Rare het report has different intensities for same probeset when using probeset-ids file vs cdf.
Changed some rare het parameters from developer option.
Update Rare Het Parameter Threshold Values.
apt-format-results -export-vcf-file: INDEL position is off by 1.
When enabled, there will be 2 additional output files: AxiomGT1.rare_het.report and AxiomGT1.rare_het_maj_hom.report. When turned on, if the heterozygous call fails the rare hetĪdjustment test, it will be changed to a ‘NoCall’. The parameter ‘do-rare-het-adjustment’ is defaulted to ‘false’. The genotyping algorithm has been updated to include option of using a set of parameters for rare heterozygous calling.
Bug fix: For VCF File export, the INDEL position is off by 1.
Bug fix: Allele Translation will now run to completion even if there are samples in the batch that have many haploid No Calls.
The 2.11.3 release of APT enables use of a set of metrics to distinguish rare heterozygous genotyping calls for the Axiom family of arrays.
Fix to fseek in runing apt-summary-genotype-axiom.
Fix to segmentation fault running cnvmix.
Fix to apt-package-util crash when input genotyping data directory contains and files at the same level.
New output files for "Remote Copy Number-Influenced" Genotyping added to CNVmix.
Fix to apt-package-util so that it does not return zero exit code when application finished with error.
Fix to apt2-sdk to check the return values of client call backs.
Fix to the pption which did not work correctly.
bug fix: previously an “fseek” error would occur if probeset_id file had probesets sorted in different order than the summary.txt file.
Enable HMM output to be packaged into batches suitable for viewing in AxAS 5.0 or higher.
The 2.11.4 release of APT is a point release to update apt-package-util to package HMM output into Axiom Analysis Suite compatible batches and to fix a defect in apt-summary-genotype.
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